#!/usr/bin/env ruby

$:<< File.expand_path(File.join(File.dirname(File.dirname __FILE__),"lib"))
require 'bio-pipengine'

banner_text = "\nLauncher for Complex Biological Pipelines . Copyright(C) 2012 Francesco Strozzi, Raoul Jean Pierre Bonnal\n\n" 
version_text = File.read File.expand_path(File.join(File.dirname(File.dirname __FILE__),"VERSION"))
SUB_COMMANDS = %w(run jobs)


#Bio::Pipengine.check_config

options = {}
cmd = ARGV.first # get the subcommand
opts = case cmd
when "run" 	
	options[:run] = true
	ARGV.shift
	Trollop::options do
		opt :pipeline, "YAML file with pipeline and sample details", :short => "p", :type => :string, :default => "pipeline.yml"
		opt :samples_file, "YAML file with samples name and directory paths", :short => "f", :type => :string, :default => "samples.yml"
		opt :samples, "List of sample names to run the pipeline", :type => :strings, :short => "l"
		opt :steps, "List of steps to be executed", :type => :strings, :short => "s"
		opt :dry,"Dry run. Just create the job script without submitting it to the batch system", :short => "d"
		opt :tmp, "Temporary output folder", :type => :string, :short => "t"
		opt :create_samples, "Create samples.yml file from a Sample directory (only for CASAVA projects)", :short => "c", :type => :strings
		opt :multi, "List of samples to be processed by a given step (the order matters)", :short => "m", :type => :strings
		opt :group, "Specify the group of samples to run the pipeline steps on (do not specify --multi)", :short => "g", :type => :string
		opt :allgroups, "Apply the step(s) to all the groups defined into the samples file", :short => "a"
		opt :name, "Analysis name", :short => "n", :type => :string
		opt :output_dir, "Output directory (override standard output directory names)", :short => "o", :type => :string
		opt :pbs_opts, "PBS options", :type => :strings, :short => "b"
		opt :pbs_queue, "PBS queue", :type => :string, :short => "q"
		opt :inspect_pipeline, "Show steps", :short => "i", :type => :string
		opt :log, "Log script activities, by default stdin. Options are fluentd", :type => :string, :default => "stdin"
		opt :log_adapter, "(stdin|syslog|fluentd) In case of fluentd use http://destination.hostname:port/yourtag", :type => :string
		opt :tag, "Overwrite tags present in samples.yml and pipeline.yml files (e.g. tag1=value1 tag2=value2)", :type => :strings
	end
when "-h"
	puts banner_text
	puts "List of available commands:\n\trun\tSubmit pipelines to the job scheduler\n"
	exit
else
	global_opts = Trollop::options do
		banner banner_text
		version "PipEngine v#{version_text}"
	  puts banner_text
		puts "PipEngine v#{version_text}" 
		puts "List of available commands:\n\trun\tSubmit pipelines to the job scheduler\n\n"
	end
end



options = options.merge opts
Trollop::die :multi, "Specifing both --group and --multi is not allowed" if options[:multi] and options[:group]

if options[:create_samples]
	Bio::Pipengine.create_samples options[:create_samples]
#elsif options[:jobs]
#	if options[:job_id] 
#		Bio::Pipengine.show_stats(options[:job_id])
#	elsif options[:job_name]
#		warn "Not yet implemented"
#		exit
#	elsif options[:delete]
#		if options[:delete].empty?
#			warn "Provide one or more Job IDs or write 'all' to delete all your running jobs".red
#			exit
#		end
#		puts "Warning: this will delete the following running jobs: ".light_blue + "#{options[:delete].join(",")}".green
#		print "Are you sure? (y|n):"
#		answer = gets.chomp
#		if answer == "y"
#			Bio::Pipengine.delete_jobs(options[:delete])
#		else
#			puts "Aborting..."
#			exit
#		end
#	else
#		Bio::Pipengine.show_stats(["all"])
#	end
elsif options[:pipeline] && options[:samples_file]
	if options[:inspect_pipeline]
		Bio::Pipengine.inspect_steps(options[:inspect_pipeline])
		exit
	else
		abort("File not found: #{options[:pipeline]}".red) unless File.exists? options[:pipeline]
		abort("File not found: #{options[:samples_file]}".red) unless File.exists? options[:samples_file]
		abort("Please provide a valid step name with the --step parameter".red) unless options[:steps]
		if options[:allgroups]
			Bio::Pipengine.load_samples_file(options[:samples_file])["samples"].keys.each do |group|
				options[:group] = group
				Bio::Pipengine.run(options)	
			end
		else
			Bio::Pipengine.run(options)
		end
	end
end